2025
Alas CD, Wu L, Pinaud F, Haselwandter CA. 2025. Diffusion-driven self-assembly of emerin nanodomains at the nuclear envelope. Phys. Rev. Research 7:L012019.
Cai S, Mai J, Hong W, Fraser SE, Cutrale F. 2025. Rapid diffused optical imaging for accurate 3D estimation of subcutaneous tissue features. iScience 28.
Chen S, Phillips CM. 2025. Nuclear Argonaute protein NRDE-3 switches small RNA partners during embryogenesis to mediate temporal-specific gene regulatory activity. eLife 13:RP102226.
Cherchia L, Fraser SE, Schneider F, Finley SD. 2025. BPS2025 – A tale of trafficking: On prolactin receptor localization in pancreatic β-cells. Biophysical Journal 124:484a.
Dean MD, Ghione CR, Lough-Stevens M. 2025. The lifespan of corpora lutea in nonpregnant females is positively correlated with gestation length. Journal of Mammalogy 106:506–512.
Ghione CR, Dean MD. 2025. Sexual size dimorphism correlates with the number of androgen response in mammals, but only in small-bodied species. Genome Biology.
Ito F, Li Z, Minakhin L, Khant HA, Pomerantz RT, Chen XS. 2025. Structural Basis for Polθ-Helicase DNA Binding and Microhomology-Mediated End-Joining. bioRxiv 19:3725.
Mattins F, Nagrath S, Fan Y, Manea TKD, Das S, Shankar A, Tower J. 2025. Machine learning scoring reveals increased frequency of falls proximal to death in Drosophila melanogaster. The Journals of Gerontology, Series A: Biological Sciences and Medical Sciences:glaf029.
Orengo C, Ehrenreich IM, Marcotte EM, Kolodny R, Ben-Tal N, de Boer CG, McWhite CD, Ranganathan R, Honig B, Bromberg Y, Thornton JW. 2025. What can recent methodological advances help us understand about protein and genome evolution?. Cell Systems 15.
Schneider F, Cuala J, Pan Y, Fuente OA de la, Cherchia L, Fraser SE. 2025. BPS2025 – Navigating cross-excitation: Multiplexing NADH and fluorescent proteins in metabolic imaging. Biophysical Journal 124:161a.
Sebastian H, Robador A, Ray D, Angermeyer A, D’Hondt S, Huber JA, Finkel SE. 2025. Identifying Potential Nutrient Acquisition Mechanisms of for Long-Term Survival: Adaptive Evolution of Halomonas Isolated from Subseafloor Crustal Fluids. Front. Microbiol. 16.
Tyson AS, Khan S, Motiwala Z, Han GW, Zhang Z, Ranjbar M, Styrpejko D, Ramos-Gonzalez N, Woo S, Villers K, Gati C. 2025. Molecular mechanisms of inverse agonism via κ-opioid receptor–G protein complexes. Nature Chemical Biology:1–12.
Wang Z, Gurlo T, Satin LS, Fraser SE, Butler PC. 2025. Subcellular Compartmentalization of Glucose Mediated Insulin Secretion. Cells 14:198.
Wu L, Pinaud F. 2025. BPS2025-Nanoscale imaging of SUN1 LINC complex organization during nuclear mechanics. Biophysical Journal 124:143a.
Zhai D, Pinaud F. 2025. BPS2025-Investigating emerin self-association in vitro using single-molecule FRET. Biophysical Journal 124:630a.
2024
Alnajjar KS, Wang K, Alvarado-Cruz I, Chavira C, Negahbani A, Nakhjiri M, Minard C, Garcia-Barboza B, Kashemirov BA, McKenna CE, Goodman MF, Sweasy JB. 2024. Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase β. Biochemistry 63:1412–1422.
Amacker A, Peng C-C, Jiang, Nan, Sirivolu S, Higa N, Stachelek K, Reiser B, Kuhn P, Cobrinik D, Neviani P, Berry JL, Xu L, Jovanovic-Talisman T. 2024. Phenotypic biomarkers of aqueous extracellular vesicles from retinoblastoma eyes. Journal of Molecular Markers 25:11660.
Archambeau A, Barekatain M, Wang Z, Cherezov V, Fraser SE, White KL, Hayes MA. 2024. Investigating the use of direct current insulator-based dielectrophoresis to study insulin vesicle subpopulations. Biophysical Journal 123:105a.
Bagheri P, Eremina OE, Fernando A, Kamal M, Stegis I, Vazquez C, Shishido SN, Kuhn P, Zavaleta C. 2024. A Systematic Approach toward Enabling Maximal Targeting Efficiency of Cell Surface Proteins with Actively Targeted SERS Nanoparticles. ACS Appl. Mater. Interfaces 16:15847–15860.
Bai L, Courcoubetis G, Mason J, Hicks JB, Nieva J, Kuhn P, Shishido SN. 2024. Longitudinal tracking of circulating rare events in the liquid biopsy of stage III–IV non-small cell lung cancer patients. Discov Onc 15:142.
Barekatain M, Liu Y, Archambeau A, Cherezov V, Fraser S, White KL, Hayes MA. 2024. Insulator-based dielectrophoresis-assisted separation of insulin secretory vesicles.Ailion M, Malhotra V, Ailion M, Kreutzberger AJ, editors. eLife 13:e74989.
Berry JL, Pike S, Shah R, Reid MW, Peng C-C, Wang Y, Yellapantula V, Biegel J, Kuhn P, Hicks J. 2024. Aqueous humor liquid biopsy as a Companion diagnostic for retinoblastoma: implications for diagnosis, prognosis, and Therapeutic options: five years of progress. American journal of ophthalmology 263:188–205.
Chen S, Phillips CM. 2024a. Silencing of a NRDE-3 transgene in C. elegans germ cells and early embryos is mediated by the RNAi pathway. microPublication 2024:10.17912.
Chen S, Phillips CM. 2024b. HRDE-2 drives small RNA specificity for the nuclear Argonaute protein HRDE-1. Nature Communications 15:957.
Cherchia L, Schneider F, Finley SD, Fraser SE. 2024. Integrating mechanistic modeling and quantitative imaging to reveal pancreatic beta cell signaling dynamics. Biophysical Journal 123:411a–412a.
Choi HY, Zhu Y, Zhao X, Mehta S, Hernandez JC, Lee J-J, Kou Y, Machida R, Giacca M, Del Sal G, Chen L. 2024. NOTCH localizes to mitochondria through the TBC1D15-FIS1 interaction and is stabilized via blockade of E3 ligase and CDK8 recruitment to reprogram tumor-initiating cells. Experimental & Molecular Medicine 56:461–477.
Chung CS, Kou Y, Shemtov SJ, Verheijen BM, Flores I, Love K, Del Dosso A, Thorwald MA, Liu Y, Hicks D, Benayoun BA, Chen L. 2024. Transcript errors generate amyloid-like proteins in human cells. Nature Communications 15:8676.
Dai S, Guo L, Dey R, Guo M, Zhang X, Bates D, Cayford J, Jiang L, Wei H, Chen Z, Chen L. 2024. Structural insights into the HDAC4–MEF2A–DNA complex and its implication in long-range transcriptional regulation. Nucleic Acids Research 52:2711–2723.
Dorff TB, Blanchard MS, Adkins LN, Luebbert L, Leggett N, Shishido SN, Macias A, Del Real MM, Dhapola G, Egelston C, Kuhn P. 2024. PSCA-CAR T cell therapy in metastatic castration-resistant prostate cancer: a phase 1 trial. Nature medicine 30:1636–1644.
Fixman B, Díaz-Gay M, Qiu C, Margaryan T, Lee B, Chen XS. 2024. Validation of the Apobec3a-Mediated Rna Single Base Substitution Signature. Journal of Molecular Biology 436.
Forsburg SL. 2024. The micromammals. G3: Genes, Genomes, Genetics 14:jkae073.
Fraser SE, Pudavar H, Reddington J, Junge JA, Lin J, Ossato G. 2024. STELLARIS 8 DIVE: a rainbow of possibilities with multiphoton excitation and lifetime-based information. Multiphoton Microscopy in the Biomedical Sciences 12847:32–33.
Hale JJ, Matsui T, Goldstein I, Mullis MN, Roy KR, Ville CN, Miller D, Wang C, Reynolds T, Steinmetz LM, Ehrenreich IM. 2024. Genome-scale analysis of interactions between genetic perturbations and natural variation. Nature Communications 15:4234.
Harden M, Kovalev M, Molano G, Yorke C, Miller R, Reed D, Alberto F, Koos DS, Lansford R, Nuzhdin S. 2024a. Heat stress analysis suggests a genetic basis for tolerance in Macrocystis pyrifera across developmental stages. Communications Biology 7:1147.
Harden M, Kovalev M, Molano G, Yorke C, Miller R, Reed D, Alberto F, Koos DS, Lansford R, Nuzhdin S. 2024b. Author Correction: Heat stress analysis suggests a genetic basis for tolerance in Macrocystis pyrifera across developmental stages. Communications Biology 7:1639.
Higa N, Welter L, Xu L, Kolatkar A, Bramlett KS, Gjoerup OV, Graf R, Huang RS, Leary RJ, Lee Y, Kuhn P. 2024. Liquid Biopsy Profiling with Multiple Tests in Patients with Metastatic Breast Cancer. Journal of Molecular Pathology 5:199–214.
Huang WYC, Ferrell JE, Cheng X. 2024. Measuring Molecular Diffusion in Self-Organizing Xenopus Extracts by Fluorescence Correlation Spectroscopy. In: Castro A, Lacroix B, editors. Cell Cycle Control. Vol. 2740. Methods in Molecular Biology. New York, NY: Springer US. p. 107–115.
Isdaner AJ, Levis NA, Ehrenreich IM, Pfennig DW. 2024. Genetic variants underlying plasticity in natural populations of spadefoot toads: environmental assessment versus phenotypic response. Genes 15:611.
Ithnin M, Vu WT, Marjuni M, Amiruddin MD, Singh A, Suryawanshi V, Serdari NM, Zaki NM, Nuzhdin SV, Chang PL. 2024. Elaeis species specific SNPs allow authentication of natural hybrids in a wild E. oleifera germplasm collection. Biocatalysis and Agricultural Biotechnology 60:103304.
Ito F, Li Z, Minakhin L, Chandramouly G, Tyagi M, Betsch R, Krais JJ, Taberi B, Vekariya U, Calbert M, Skorski T, Johnson N, Chen XS, Pomerantz RT. 2024. Structural basis for a Polθ helicase small-molecule inhibitor revealed by cryo-EM. Nat Commun 15:7003.
Ito F, Yang H, Zhou ZH, Chen XS. 2024. Structural basis for polyuridine tract recognition by SARS-CoV-2 Nsp15. Protein & Cell 15:547–552.
Jaszczur MM, Pham P, Ojha D, Pham CQ, McDonald JP, Woodgate R, Goodman MF. 2024. Pathogen-encoded Rum DNA polymerase drives rapid bacterial drug resistance. Nucleic Acids Research 52:12987–13002.
Kerman BE, Junge JA, Fayzullina M, Wang J, Yang LZ, Meuret CJ, Mertens J, Seidler P, Fraser S, Yassine HN. 2024. Studying APOE Aggregation in Live Cells and Human Neurons. Alzheimer’s & Dementia 20:e092614.
Kingsley SF, Seo Y, Wood A, Wani KA, Gonzalez X, Irazoqui J, Finkel SE, Tissenbaum HA. 2024. Glucose-fed microbiota alters C. elegans intestinal epithelium and increases susceptibility to multiple bacterial pathogens. Sci Rep 14:13177.
Landis GN, Baybutt B, Shoham S, Fan Y, Olsen K, Tower J, Yan K. 2024. Mifepristone and rapamycin have non-additive benefits for life span in mated female Drosophila. Fly 18:2419151.
Landis GN, Bell HS, Peng OK, Fan Y, Yan K, Baybutt B, Tower J. 2024. Conditional Inhibition of Eip75B Eliminates the Effects of Mating and Mifepristone on Lifespan in Female Drosophila. Cells 13:1123.
Li T, Petreaca RC, Forsburg SL. 2024. Chromodomain mutation in S. pombe Kat5/Mst1 affects centromere dynamics and DNA repair. Plos one 19:e0300732.
Lin W, Tseng K, Fraser SE, Junge J, White KL. 2024. Decoding Insulin Secretory Granule Maturation Using Genetically Encoded pH Sensors. ACS Sens. 9:6032–6039.
Luu P, Fraser SE, Schneider F. 2024. More than double the fun with two-photon excitation microscopy. Commun Biol 7:1–15.
Marshall AG, Neikirk K, Stephens D, Garza-Lopez E, Vue Z, Beasley HK, Doe YJ, Campbell D, Fears L, Alghanem A, Spencer EC, Scudese E, Owens B, Vang C, Morton DJ, Conley Z, Hinton A. 2024. A workshop to showcase the diversity of scientists to middle school students. Advances in Physiology Education 48:186–192.
Mason J, Shishido SN, Courcoubetis G, Tessone D, Liljegren E, Naghdloo A, Hicks J, Nieva JJ, Kuhn P. 2024. Mathematical oncology in the context of early breast cancer detection. Cancer Research 84:6076–6076.
Merigliano C, Palumbieri MD, Lopes M, Chiolo I. 2024. Replication forks associated with long nuclear actin filaments in mild stress conditions display increased dynamics. microPublication biology 2024:10–17912.
Michael M, Belew M, Chien E, Wong M. 2024. The topoisomerase II/condensin II axis silences transcription during germline specification in Caenorhabditis elegans. G3: Genes, Genomes, Genetics 14:jkae236.
Neikirk K, Vue Z, Vue N, Barongan T, Vang C, Beasley HK, Marshall AG, Kirabo A, Wanajalla CN, Smith N, Morton D, Shuler HD, Hinton A. 2024. Disparities in funding for Nobel Prize awards in medicine and physiology across nationalities, races, and gender. Journal Cellular Physiology 239:e31157.
Osborne MG, Simons AL, Molano G, Tolentino B, Singh A, Arismendi GJM, Alberto F, Nuzhdin SV. 2024. Investigating the relationship between microbial network features of giant kelp “seedbank” cultures and subsequent farm performance. Plos one 19:e0295740.
Park JM, Forsburg SL. 2024. Analysis of transcriptional response in haploid and diploid Schizosaccharomyces pombe under genotoxic stress. G3: Genes, Genomes, Genetics 14:jkae177.
Parra A, Denkova D, Burgos-Artizzu XP, Aroca E, Casals M, Godeau A, Ares M, Ferrer-Vaquer A, Massafret O, Oliver-Vila I, Mestres E, Acacio M, Costa-Borges N, Rebollo E, Chiang HJ, Fraser SE, Cutrale F, Seriola A, Ojosnegros S. 2024. METAPHOR: Metabolic evaluation through phasor-based hyperspectral imaging and organelle recognition for mouse blastocysts and oocytes. Proceedings of the National Academy of Sciences 121:e2315043121.
Parreno V, Loubiere V, Schuettengruber B, Fritsch L, Rawal CC, Erokhin M, Győrffy B, Normanno D, Di Stefano M, Moreaux J, Butova NL, Chiolo I, Chetverina D, Martinez AM, Cavalli G. 2024. Transient loss of Polycomb components induces an epigenetic cancer fate. Nature 629:688–696.
Pham P, Wood EA, Dunbar EL, Cox MM, Goodman MF. 2024. Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements. Nucleic Acids Research 52:6392–6405.
Pollalis D, Calle AG, Martinez-Camarillo JC, Ahluwalia K, Hinman C, Mitra D, Lebkowski J, Lee SY, Thomas BB, Ahmed F, Chan V, Junge JA, Fraser S, Louie S, Humayun M. 2024. Scaling up polarized RPE cell supernatant production on parylene membrane. Experimental Eye Research 240:109789.
Rawal CC, Loubiere V, Butova NL, Gracia J, Parreno V, Merigliano C, Martinez A-M, Cavalli G, Chiolo I. 2024. Sustained inactivation of the Polycomb PRC1 complex induces DNA repair defects and genomic instability in epigenetic tumors. Histochem Cell Biol 162:133–147.
Resnick K, Shah A, Mason J, Kuhn P, Nieva J, Shishido SN. 2024. Circulation of rare events in the liquid biopsy for early detection of lung mass lesions. Thoracic Cancer 15:2100–2109.
Ryu T, Merigliano C, Chiolo I. 2024. Nup153 is not required for anchoring heterochromatic DSBs to the nuclear periphery. microPublication biology 2024:10–17912.
Seo J, Shishido SN, Mason J, Velasco CR, Chen A, Rothwell D, Crosbie P, Hicks J, Dive C, Kuhn P. 2024. Peripheral blood liquid biopsy for the screening of lung cancer. Cancer Research 84:7489–7489.
Shishido SN, Hart O, Jeong S, Moriarty A, Heeke D, Rossi J, Bot A, Kuhn P. 2024. Liquid biopsy approach to monitor the efficacy and response to CAR-T cell therapy. Journal for Immunotherapy of Cancer 12:e007329.
Shishido SN, Kuhn P, Suresh D, Courcoubetis G, Ye B, Lin E, Mason J, Park K, Lewis M, Wang R, Lo SK. 2024. Determining the efficacy of ExThera Seraph100 blood filtration in patients diagnosed with pancreatic cancer through the liquid biopsy. BJC reports 2:47.
Shishido SN, Lin E, Nissen N, Courcoubetis G, Suresh D, Mason J, Osipov A, Hendifar AE, Lewis M, Gaddam S, Kuhn P. 2024. Cancer-related cells and oncosomes in the liquid biopsy of pancreatic cancer patients undergoing surgery. npj Precision Oncology 8:36.
Shishido SN, Marvit A, Pham D, Luo T, Xu L, Mason J, Priceman SJ, Portnow J, Kuhn P. 2024. Multi-Omic Characterization of Single Cells and Cell-Free Components Detected in the Cerebrospinal Fluid of Patients with Leptomeningeal Disease. Cancers 16:3746.
Shishido SN, Marvit A, Priceman S, Portnow J, Kuhn P. 2024. Liquid biopsy of cerebrospinal fluid in breast to brain metastases. Cancer Research 84:2296–2296.
Sirivolu S, Schmidt MJ, Prabakar RK, Kuhn P, Hicks J, Berry JL, Xu L. 2024. Single-cell somatic copy number alteration profiling of vitreous humor seeds in retinoblastoma. Ophthalmic Genetics 45:646–649.
Suresh DD, Courcoubetis G, Lin E, Mason J, Nissen N, Gaddam S, Lo S, Pandol S, Kuhn P, Shishido S. 2024. Determining the efficacy of blood filtration in patients diagnosed with pancreatic cancer through the liquid biopsy. Cancer Research 84:3710–3710.
Tolentino B, Nuzhdin S. 2024. Eight complete genome sequences of bacteria isolated from laboratory stock of giant kelp gametophytes.Stewart FJ, editor. Microbiol Resour Announc 13:e00984-23.
Tower J. 2024. Selectively advantageous instability in biotic and pre-biotic systems and implications for evolution and aging. Front. Aging 5.
Vissers C, Lindell SR, Nuzhdin SV, Almada AA, Timmermans K, Nuzhdin S. 2024. Using sporeless sporophytes as a next step towards upscaling offshore kelp cultivation. J Appl Phycol 36:313–320.
Vue Z, Vang C, Wanjalla CN, Marshall AG, Neikirk K, Stephens D, Perales S, Garza-Lopez E, Beasley HK, Kirabo A, Doe YJ, Campbell D, Fears L, Alghanem A, Scudese E, Owens B, Morton DJ, Williams CR, Conley Z, Antentor H. 2024. A workshop to enrich physiological understanding through hands-on learning about mitochondria-endoplasmic reticulum contact sites. Advances in Physiology Education 48:808–817.
Winter CM, Szekely P, Popov V, Belcher H, Carter R, Jones M, Fraser SE, Truong TV, Benfey PN. 2024. SHR and SCR coordinate root patterning and growth early in the cell cycle. Nature 626:611–616.
Xu J, Lei X, Li A, Li J, Li S, Chen L. 2024. Scalable production of recombinant three-finger proteins: from inclusion bodies to high quality molecular probes. Microb Cell Fact 23:48.
Yadav R, Gati C. 2024. Packaging monoamine neurotransmitters. Cell Research 34:185–186.
Yadav R, Yadav MK, Maharana J, Saha S, Sarma P, Banerjee R, Shukla AK, Gati C. 2024. Structural basis of anaphylatoxin receptor activation and signaling bias. Biophysical Journal 123:22a.
Yang Y, Braga MV, Dean MD. 2024. Insertion–Deletion Events Are Depleted in Protein Regions with Predicted Secondary Structure. Genome Biology and Evolution 16:evae093.
Zang PD, Blanchard S, Martirosyan H, Adkins L, Dhapola G, Shishido S, Young C, Karam H, Stiller T, D’Apuzzo M, Kuhn P, Forman SJ, Priceman S, Dorff TB. 2024. A phase 1b study of PSCA CAR T cells plus or minus radiation for the treatment of patients with PSCA+ metastatic castration-resistant prostate cancer. JCO 42:TPS5112–TPS5112.
Zhou H, Li I, Wang B, Bramlett CS, Shen K, Hao J, Yen DP, Ando Y, Lu R, Shen K, Fraser SE. 2024. Label-free metabolic optical biomarkers track stem cell fate transition in real time. Science Advances 10:eadi6770.